The serpulid polychaete, Hydroides elegans is a problem fouler in warm water ports throughout the world and is an excellent candidate for investigating molecular reception during larval settlement and metamorphosis. H. elegans is induced to settle and metamorphose when given the appropriate bacterial cue. This study utilized transcriptome sequencing of H. elegans and genome sequencing of two inductive bacterial strains (i.e., Pseudoalteromonas luteoviolacea and Cellulophaga lytica) to provide a means to examine mechanisms and/or genes that may be significant in understanding the interaction between bacteria and larvae that result in biofouling. Transcriptome analysis and in-situ hybridization techniques determined the genetic expression and location of genes in H. elegans as well as important biological pathways involved in metamorphic competence. Likewise, the genome sequencing of P. luteoviolacea and C. lytica determined significant coding sequences for structures that play a role in the settlement and metamorphosis of H. elegans.